Laboratory VI
Code: 100975 ECTS Credits: 3| Degree | Type | Year | Semester |
|---|---|---|---|
| 2500502 Microbiology | OB | 3 | 2 |
Contact
- Name:
- Neus Ferrer Miralles
- Email:
- Neus.Ferrer@uab.cat
Use of Languages
- Principal working language:
- catalan (cat)
- Some groups entirely in English:
- No
- Some groups entirely in Catalan:
- No
- Some groups entirely in Spanish:
- No
Other comments on languages
Half of classes are given in Spanish and the other half in CatalanTeachers
- Jordi Mas Castella
- Andromeda Celeste Gomez Camacho
- Daniel Yero Corona
- Nuria Vigues Frantzen
Prerequisites
Students are advised to review the scientific-theoretical contents in which this subject is based.
It is also appropriate that this subject is taken simultaneously or subsequently to other subjects scheduled for the second semester of the third year of the Microbiology degree.
To take this course, students must have passed the safety and biosafety tests available in the corresponding educational space of the Campus Virtual or Moodle.
The information to overcome these tests is in the communication area of the Microbiology degree. Furthermore, it is essential for students to follow the work rules as directed by teachers and to accept and follow the rules of operation of the teaching laboratories of the Faculty of Biosciences.
For security reasons, If any of the tests have not been passed or the student does not bring a labcoat and safety glasses will not be allowed to enter the laboratory.
Objectives and Contextualisation
It is a compulsory third year Bachelor of nuclear Microbiology, which introduces students to the use of a set of basic microbiology techniques for experimentation in a laboratory Industrial Microbiology and Environmental Microbiology.
The knowledge gained in this course will enable students to acquire skills in other subjects or theoretical practices that make up the degree of Microbiology and are scheduled to be taken simultaneously or after that.
The specific objectives to be achieved are defined as follows and will allow students to:
1. Isolate and select microorganism of industrial interest.
2. Handle a microorganism to convert it into a producer of a product of industrial interest using molecular methods.
3. Develop a process for obtaining a product of industrial interest.
4. Determine the microbiological quality of the air and surfaces in industrial facilities.
5. Determine the microbiological quality of water.
6. Describe the disinfectant effect of chemicals.
7. Convert industrial waste into products with high protein content.
8. Select and evaluate the activity of microorganisms involved in bioremediation of soils.
9. Demonstrate the activity of bacteria inhibiting the growth of fungal pathogens.
Competences
- Adapt to new situations.
- Apply knowledge of theory to practice
- Apply the principles of risk assessment and prevention in the laboratory, and biosafety regulations on microorganisms and manipulation of different biological systems.
- Apply tools based on microorganisms to assess the environmental impact of human activity, and to recover contaminated environments.
- Assess the quality and/or microbiological safety of foods, water, drugs, cosmetics and other natural or artificial products.
- Characterise the causal agents of microbial diseases in humans, animals and plants in order to diagnose and control them, perform epidemiological studies and be aware of present-day problems with these diseases and strategies to combat them.
- Design and control processes of microbial origin and participate in productive processes in which microorganisms intervene.
- Design and use disinfection and sterilisation treatments and also methods for assessing their effectiveness.
- Develop critical reasoning skills in the field of study and in relation to the social context.
- Display a capacity for analysis, synthesis, organisation, planning and decision-making.
- Display sensibility towards environmental, health and social matters.
- Know and apply safety and quality regulations in microbiology.
Learning Outcomes
- Adapt to new situations.
- Analyse and monitor the population dynamics. of microorganisms in applied processes.
- Apply biosafety regulations in the laboratory.
- Apply disinfection treatments and evaluate their efficiency.
- Apply in the laboratory the principles of risk assessment and prevention.
- Apply knowledge of theory to practice
- Apply methods for evaluating the potential for disinfection of chemical products.
- Assess the effect of disinfectants on microorganisms and work surfaces.
- Calculate the yield of microorganisms grown in different substrates.
- Design strategies for bioremediation and biorecovery based on model systems developed in the laboratory.
- Determine levels of atmospheric microbial contamination.
- Develop critical reasoning skills in the field of study and in relation to the social context.
- Display a capacity for analysis, synthesis, organisation, planning and decision-making.
- Display sensibility towards environmental, health and social matters.
- Establish the optimal conditions for products of microbial origin.
- Evaluate biological activity in microbial products.
- Evaluate the microbial load of surfaces.
- Experimentally determine and interpret the kinetic parameters that define microbial growth.
- Experimentally determine the parameters for defining sterilisation treatments.
- Isolate and characterise potential biological control agents based on microorganisms for the control of pests and diseases.
- Isolate and cultivate microorganisms of interest in biotechnology.
- Know and apply safety and quality regulations in microbiology.
- Select microbial communities for the treatment of contaminants.
- Use bioindicators to assess environmental impacts.
- Use continuous- and discontinuous-operation bioreactors.
- Use microorganisms to evaluate the degree of contamination of the medium and recover it.
- Use suitable instruments for the monitoring and control of processes based on microorganisms.
Content
The course is divided into the following sections:
Section 1: Industrial Microbiology
Section 2: Environmental Microbiology
Each section takes approximately 24 hours.
Section 1: Industrial Microbiology
Content: This section consists of seven sessions focusing on the isolation and the use of microorganisms to obtain products of industrial interest. Lab work in this section will be performed under the safety and biosafety regulations indicated at the beginning of each session.
1. Isolation and selection of microorganisms of industrial interest-MI1
2. Screening for activity-MI2
3. Isolation of genes of industrial interest-MI3
4. Cloning of overexpression vector-MI4
5. Development of-production method MI5
6. Evaluation-MI6
Section 2: Environmental Microbiology
Content: This section consists of eight sessions focusing on detection of the microbial environmental contamination, the use of microorganisms in bioremediation and valorisation of waste, as well as in plague control and plant diseases.
1.- Waste management
-Bioremediation in contaminated soil-MA1
-Production of unicellular protein starting from a residue-MA2
2.- Control of the environmental pollution
-Air and surface quality in industrial facilities-MA3
-Microbiological quality of water-MA4
-Desinfection of surfaces-MA5
3.- Biological control
-Isolation of bacteria from the phylosphere.
-Determination of their potential as natural enemies of plant pathogens -MA6
The contents per session that will be taught in each of the modules are the following:
Section 1: Industrial Microbiology
|
Content |
Session |
Activities |
|
MI1 |
1 |
-Enrichment and isolation of Actinomycetes from soil samples |
|
|
2 |
-Enrichment and isolation of Bacillus from soil samples -Identification, counting and isolation of Actinomycetes clones |
|
|
3 |
-Identification, counting and isolation of Bacillus clones |
|
MI2 |
3 |
-Detection of the antibiotic activity of Actinomycetes-plating -Detection of the enzymatic activity of Actinomycetes-plating |
|
|
4 |
-Detection of the antibiotic activity of Bacillus-plating -Detection of the enzymatic activity of Bacillus-plating |
|
|
5 |
-Evaluation of the enzymatic activity of Actinomycetes -Detection of the enzymatic activity of Actinomycetes-double layered plating |
|
|
6 |
-Detection of the enzymatic activity of Bacillus-double layered plating |
|
|
7 |
-Evaluation of the antibiotic activity of Bacillus -Evaluation of the enzymatic activity of Bacillus -Evaluation of the antibiotic activity of Actinomicetos -Evaluation and discussion of results |
|
MI3 |
1 |
-Purification of genomic DNA of Bacillus -PCR to amplify genes of industrial interest |
|
|
2 |
-Agarose gel to determine the DNA amplification of the gene of industrial interest |
|
MI4 |
2 |
-Restriction enzyme digestion of the E. coli expression vector -Restriction enzyme digestion of DNA fragments containing the gen industrial interest -Dephosphorilation and purification of hte linearized E. coli expression vector |
|
|
3 |
-Ligatio of hte gene of industrial interest -Transformation of hte ligation reaction |
|
|
4 |
-Detection of productive transformants |
|
MI5 |
5 |
-Inoculation of productive microorganisms of enzymatic activities of industrial interest |
|
|
6 |
-Batch experiment: reinoculation of the culture and growth curve monitoring of microorganisms producing enzymatic activities of industrial interest |
|
MI6 |
6 |
-Evaluation of the production and activity of enzymes of industrial interest produced by microorganisms |
|
|
7 |
-Evaluation and discussion of results |
Section 2: Environmental Microbiology
|
Content |
Session |
Activities |
|
MA1 |
4 |
-Enrichment and isolation of hydrocarbon-degrading bacteria from contaminated soil samples -Determination of the microbial activity of contaminated soil samples |
|
|
8 |
-Reading total heterotrophs -Detection of total hydrocarbon degrading microorganisms -Detection and enumeration of microorganisms degrading polycyclic aromatic hydrocarbons -Detection of n-hexadecane degrading microorganisms |
|
|
9 |
-Enumeration of total hydrocarbon degrading microorganisms -Enumeration of n-hexadecane degrading microorganisms -Evaluation and discussion of results |
|
MA2 |
1 |
-Inoculation of bioreactors with microorganisms in media with different concentrations of sugars -Initial sampling of the culture: viable cell plating, sugars, OD -Analysis of samples: viable cell plating, OD |
|
|
2 |
-Sampling of the culture: viable cell plating, sugars, OD -Analysis of samples: viable cell counting, growth rate of the culture, doubling time, OD, determination of sugar consumption |
|
|
3 |
Final sampling of the culture: -Analysis of the samples: -Cell counting and graphs -Determination of sugar consumption -Determination of the biomass of the culture -Calculations -Evaluation and discussion of results |
|
MA3 |
5 |
-Detection of microorganisms in air samples -Detection of microorganisms in surface samples |
|
|
7 |
-Observation and counting of microorganisms of air and surface samples -Evaluation and discussion of results |
|
MA4 |
5 |
-Plating of viable microorganisms from water samples -Detection and counts of coliform bacteria and Escherichia coli -Intestinal Enterococcal detection and counting -Detection and counts de Clostridium perfringens |
|
|
6 |
-Evaluation and test of confirmation of the presence of Escherichia coli -Evaluation and test of confirmation of the presence of Clostridium perfringens |
|
|
7 |
-Evaluation of the presence of Escherichia coli in water samples -Evaluation and test of confirmation of the presence offecal enterococci |
|
|
8 |
-Count of viable microorganisms from water samples -Evaluation and discussion of results |
|
MA5 |
6 |
-Detection of microorganisms in disinfected surface samples |
|
|
8 |
-Observation and counting of microorganisms of disinfected surfaces -Evaluation and discussion of results |
|
MA6 |
5 |
-Isolation of epiphytic bacteria from leaves of different plant species |
|
|
6 |
-Preparation of axenic cultures of leaf epiphytic bacteria |
|
|
7 |
-Conducting the biological control test of fungi by leaf epiphytic bacteria -Evaluation of the results obtained from the antagonistic potential of leaf epiphytic bacteria on a phytopathogenic fungus - Evaluation and discussion of results |
“*Unless the requirements enforced by the health authorities demand a prioritization or reduction of these contents.”
Methodology
This subject will be taught in three small groups of students (maximum 24 students per session). To be able to acquire the competences of the subject the attendance to the classes is obligatory. If a student, for reasons justified and unforeseeable (such as a health problem, death of a relative up to second degree, accident, enjoy the status of elite athlete and have a competition or sports activity of obligatory attendance, etc.) has not Attended a session / practice sessions, he/she will have to speak with the responsible teacher and present the corresponding proof as soon as possible (official medical certificate stating explicitly the inability to attend the session / Practices, police attestation, justification of the competent sports organization, etc.). In case of strike, if a student decides to exercise his/her right to strike, he/she must notify the subject coordinator within a maximum period of 48 hours after the day of the strike. In no enevent the absence shall exceed 20% of the programmed activities. The maximum absence in each of the sections (industrial or environmental microbiology) is set at a maximum of 10% to be evaluated. In the event that this value is exceeded, the subject will be qualified with a Non-Valuable.
The students will have a Manual of the subject before the beginning of the practical sessions. At each practice session it is compulsory for the student to wear his or her own lab coat, laboratory glasses, permanent marker, calculator and the Manual of the subject that will be available in the Virtual Campus, Moodle platform, or where indicated by the teachers. It is also necessary to carry a notebook (Miquelrius, Abacusor Oxford) with sewn sheets, where each student will note the laboratory observations. For the accomplishment of the practices the students will work in pairs and under the supervision of the teacher. At the beginning and/or during each session the teacher will make brief theoretical explanations of the content of the practices and procedures to be carried out by the students, as well as the specific safety measures and the treatment of the different chemical and biological waste generated.
In order to achieve a good performance and to acquire the competences corresponding to this subject it is essential that the student makes a comprehensive reading of the Manual of the subject, becoming familiar with the practices that will be carried out in each session, as well as with the methodology that will have to apply in each case.
“*The proposed teaching methodology may experience some modifications depending on the restrictions to face-to-face activities enforced by health authorities.”
Activities
| Title | Hours | ECTS | Learning Outcomes |
|---|---|---|---|
| Type: Directed | |||
| Practical Laboratory Classes | 48 | 1.92 | 1, 2, 5, 3, 6, 7, 4, 8, 20, 21, 9, 22, 12, 11, 19, 18, 10, 15, 23, 14, 13, 24, 25, 26, 27, 16, 17 |
| Type: Supervised | |||
| Tutoring | 1 | 0.04 | 1, 2, 5, 3, 6, 7, 4, 8, 20, 21, 9, 22, 12, 11, 19, 18, 10, 15, 23, 14, 13, 24, 25, 26, 27, 16, 17 |
| Type: Autonomous | |||
| Comprehensive reading of the practices laboratory manual | 5 | 0.2 | 2, 5, 3, 7, 4, 8, 20, 21, 9, 11, 19, 18, 10, 15, 23, 24, 25, 26, 27, 16, 17 |
| Drafting of laboratory notebook | 6 | 0.24 | 13 |
| Preparation of oral presentations | 3 | 0.12 | 12, 13 |
| Study | 12 | 0.48 | 2, 5, 3, 7, 4, 8, 20, 21, 9, 11, 19, 18, 10, 15, 23, 24, 25, 26, 27, 16, 17 |
Assessment
The evaluation of the subject will be done by section and will be continued. The weight of the evaluation on the final grade of the subject of each section is: Section 1 50 %, Section 2 50 %. It will be necessary to obtain a grade equal to or higher than 5 in each of the practical sections separately to be able to pass the subject.
The evaluation of each section will be carried out as follows:
Section 1.- Industrial Microbiology
Continuous assessment of group work
Oral presentation discussion of the results of the practices and participation in the practices (20 %)
Individual evaluation of the contents
Daily follow up of the notebook and work in the laboratory (10 %) Individual questionnaire with multiple choice questions (20 %)*
* The individual questionnaire can be at any time during the practice sessions and there may be more than one.
Section 2: Environmental Microbiology
Continued assessment of group work
Delivery of a final report Bioreactors (3.3 %)
Oral presentation discussion of the results of the practices and participation in the practices (6.7 %)
Individual evaluation of the contents
Daily follow-up of the laboratory book (10 %) Individual questionnaire with multiple choice questions (30 %)
In each section, the student's attitude in the laboratory, punctuality, the use of laboratory equipment (gown and goggles), compliance with the safety and biosecurity regulations, and the understanding and follow-up of the Manual of the subject will be evaluated. This assessment does not entail an increase in the score, but it can mean the reduction of up to 20% of the final mark obtained in each module.
Since attendance to the activities programmed in this subject is mandatory, the absence of any of the sessions must be justified and may not exceed 20 %. In any case, this 20 % can not be accumulated in a single section, being the maximum for each of them of 10 % absence. In the event that this value is exceeded, the student will be qualified as Not Evaluable (No Avaluable).
Students who do not pass the evaluations of the different sections of the subject will be able to recover them in the date scheduled at the end of the semester (reassessment), performing a questionnaire associated with the section not previously passed (20 and 30 % respectively for the Individual questionnaire with multiple choice questions). Remedial exams will not be scheduled for the other activities.
Students who do not obtain the minimum qualification required to pass each of the sections of the integrated laboratory, will not be able to pass the subject. In this case, the final maximum grade of the subject will be 4.
Because this subject is differentiated in modules, from the second enrollment, students will only have to evaluate the specific sections that have not been passed.
“*Student’s assessment may experience some modifications depending on the restrictions to face-to-face activities enforced by health authorities.”
Assessment Activities
| Title | Weighting | Hours | ECTS | Learning Outcomes |
|---|---|---|---|---|
| Delivery of laboratory notebook | 20 % | 0 | 0 | 2, 5, 6, 7, 4, 8, 20, 21, 9, 22, 11, 19, 18, 10, 15, 23, 13, 24, 25, 26, 27, 16, 17 |
| Evaluation of Section 1 Industrial Microbiology: multiple choice test | 20 % | 0 | 0 | 7, 4, 8, 20, 9, 11, 19, 18, 10, 23, 14, 24, 25, 26, 16, 17 |
| Evaluation of Section 1 Industrial Microbiology: oral presentation and class participation | 20 % | 0 | 0 | 12, 13 |
| Evaluation of Section 2 Environmental Microbiology: delivery of a report | 3,3 % | 0 | 0 | 2, 6, 9, 18, 10, 15, 14, 25, 27 |
| Evaluation of Section 2 Environmental Microbiology: multiple choice test | 30 % | 0 | 0 | 1, 2, 5, 3, 6, 21, 22, 12, 15, 13, 27 |
| Evaluation of Section 2 Environmental Microbiology: oral presentation and class participation | 6,7 % | 0 | 0 | 12, 13 |
Bibliography
Bibliography and web links are indicated in the corresponding sections of the laboratory manual.
Class schedules of the subject can be obtained in the information section of the Microbiology Degree website.
Industrial Microbiology
-R.S. Burlage, R. Atlas, D. Stahl, G. Geesey and G. Sayler, (1998). Techniques in Microbial Ecology. New York, NY. Oxford University Press.
-L-M. Prescott (2002). Microbiology. Capter 42: Industrial Microbiology and biotechnology, 5th Edition, New York, NY. The McGraw−Hill Companies.
-M. Rabbani, H.M. Sadeghi, F. Moazen, M. Rahimi and G. Salehi. (2011). Cloning and Expression of Randomly Mutated Bacillus subtilis α-Amylase Genes in HB101. Biotechnology Research International doi:10.4061/2011/305956.
-R.C. Cadwell andG.F. Joyce. (1994). Mutagenic PCR. Genome Res. 3: S136-S140.
-M.J. Waites, N.L. Morgan, J.S. Rockey and G. Higton (2001) Industrial Microbiology: an introduction. London, UK. Blackwell Science Ltd.
-M.R. Ladisch, N.S., Mosier, (2009) Modern Biotechnology. John Wiley & Sons, Inc. https://doi.org/10.1002/9780470473412
-Alpha amylase activity protocol: http://www.worthington-biochem.com/aa/assay.html
-Preparation of phosphate buffers: http://openwetware.org/wiki/Phosphate_buffer
Environmental Microbiology
1.-Waste treatment
-Martin Alexander (1999) Biodegradation and Bioremediation. 2nd Edition. Cornell University, Ithaca, New York, U.S.A. AcademicPress.
-Ajay Singh, Ramesh C. Kuhad, Owen P. Ward. (2009) Advances in applied bioremediation. Berlin, Heidelberg. Springer-Verlag. https://dx.doi.org/10.1007/978-3-540-89621-0
-Ralph, M. and Ji-Dong, G. (eds) (2010) Environmental Microbiology. 2nd Edition. Wiley-Blackwell. https://onlinelibrary.wiley.com/doi/book/10.1002/9780470495117
-Yates, M. V. et al. (eds) (2016) Manual of Environmental Microbiology. 4th Edition. ASM Press. doi: 10.1128/9781555818821.
2.-Control of the environmental contamination
-Wen-TsoLiu, Janet K. Caister (2010) Microbiology. Norfolk, UK. Academic Press.
-Harley−Prescott. (2002) Laboratory exercises in microbiology (5th Edition). Boston, Mass. The McGraw-Hill companies.
-Delort, A.-M. and Amato, P. (eds) (2017) Microbiology of aerosols. Wiley Blackwell. https://onlinelibrary.wiley.com/doi/book/10.1002/9781119132318
-Mohee, R. and Mudhoo, A. (eds) (2012) Bioremediation and Sustainability: Research and Applications. Wiley-Blackwell. https://onlinelibrary.wiley.com/doi/book/10.1002/9781118371220
3.-Biological control
- H.J. Benson, (2001) Microbiological applications. Laboratory manual in general microbiology (8th edition). Boston, Mass. The McGraw-Hill companies.
- B. Prapagdee, C. Kuekulvong and S. Mongkolsuk (2008). Antifungal Potential of Extracellular Metabolites Produced by Streptomyces hygroscopicus against Phytopathogenic Fungi. International Journal of Biological Sciences 4:330-337.
-Ghannoum, M. et al. (eds) (2015) Microbial Biofilms. Second Edi. ASM Press. doi: 10.1128/9781555817466.
General Microbiology
-Martín A., Béjar V., Gutierrez J.C., Llagostera M. y Quesada E. 2019. Microbiología Esencial. 1ª edición. Editorial Médica Panamericana. https://www.medicapanamericana.com/VisorEbookV2/Ebook/9788491102427